respond to comments (b2e6d13e) · Commits · 钟慕尧 / deepchem

deepchem/data/data_loader.py

+12 −17

Original line number	Diff line number	Diff line
		@@ -911,20 +911,19 @@ class FASTALoader(DataLoader):

		# Process legacy toggle
		if legacy:
		logger.info("""
		Deprecation warning: Legacy mode will soon be deprecated.
		Disable legacy mode by passing legacy=False during
		construction of FASTALoader object.
		""")
		warnings.warn(
		"""
		Legacy mode is deprecated and will be removed in
		DeepChem 3.0. Disable legacy mode by passing legacy=False
		during construction of FASTALoader object.
		""", FutureWarning)
		if featurizer is not None or auto_add_annotations:
		logger.warning(f"""
		raise ValueError(f"""
		featurizer option must be None and
		auto_add_annotations must be false when legacy mode is
		enabled. You set featurizer to {featurizer} and
		auto_add_annotations must be false when legacy mode
		is enabled. You set featurizer to {featurizer} and
		auto_add_annotations to {auto_add_annotations}.
		So we set legacy = False.
		""")
		legacy = False

		# Set attributes
		self.legacy = legacy
		@@ -1012,10 +1011,6 @@ class FASTALoader(DataLoader):
		# Handle empty sequence
		if sequence is None or len(sequence) <= 0:
		# TODO log attempts to add empty sequences every shard
		"""
		logger.info(
		"Attempting to add empty sequence, returning empty array...")
		"""
		return np.array([])
		# Annotate start/stop of sequence
		if auto_add_annotations:

+1 −4

Original line number	Diff line number	Diff line
		@@ -98,10 +98,7 @@ class OneHotFeaturizer(Featurizer):
		"""
		if self.max_length is not None:
		if (len(string) > self.max_length): # Validation
		logger.warning(
		"The length of {} is longer than `max_length`. So we return an empty array."
		)
		return np.array([])
		raise ValueError("The length of {} is longer than `max_length`.")
		string = self.pad_string(string) # Padding

		return np.array([